diff --git a/examples/computing_the_Bayes_factor.py b/examples/computing_the_Bayes_factor.py
index 76d92564b807abec9c2b33575d863b0ab8c79f9e..69129607339640302f7e1ae201711008520a69f3 100644
--- a/examples/computing_the_Bayes_factor.py
+++ b/examples/computing_the_Bayes_factor.py
@@ -24,7 +24,7 @@ nwalkers = 100
nsteps = [500, 500]
mcmc = MCMCSearch(label='computing_the_Bayes_factor', outdir='data',
- sftfilepath='data/*basic*sft', theta_prior=theta_prior,
+ sftfilepattern='data/*basic*sft', theta_prior=theta_prior,
tref=tref, tstart=tstart, tend=tend, nsteps=nsteps,
nwalkers=nwalkers, ntemps=ntemps,
log10temperature_min=log10temperature_min)
diff --git a/examples/follow_up.py b/examples/follow_up.py
index cfd8575952dbc0c4c88c6cb2c85a021e2f5db4d5..d79b9a66068a8920a76478c113a902f442d1006a 100644
--- a/examples/follow_up.py
+++ b/examples/follow_up.py
@@ -26,7 +26,7 @@ run_setup = [(1000, 50), (1000, 25), (1000, 1, False),
mcmc = pyfstat.MCMCFollowUpSearch(
label='follow_up', outdir='data',
- sftfilepath='data/*basic*sft', theta_prior=theta_prior, tref=tref,
+ sftfilepattern='data/*basic*sft', theta_prior=theta_prior, tref=tref,
minStartTime=tstart, maxStartTime=tend, nwalkers=nwalkers,
ntemps=ntemps, log10temperature_min=log10temperature_min)
mcmc.run(run_setup)
diff --git a/examples/fully_coherent_search_using_MCMC.py b/examples/fully_coherent_search_using_MCMC.py
index 4a6bdf48e8992e884298dd423e5911bc93afecb0..254f79106051b8c1bd219e14a08489246553ff67 100644
--- a/examples/fully_coherent_search_using_MCMC.py
+++ b/examples/fully_coherent_search_using_MCMC.py
@@ -53,7 +53,7 @@ nsteps = [50, 50]
mcmc = pyfstat.MCMCSearch(
label='fully_coherent_search_using_MCMC', outdir='data',
- sftfilepath='data/*'+data_label+'*sft', theta_prior=theta_prior, tref=tref,
+ sftfilepattern='data/*'+data_label+'*sft', theta_prior=theta_prior, tref=tref,
minStartTime=tstart, maxStartTime=tend, nsteps=nsteps, nwalkers=nwalkers,
ntemps=ntemps, log10temperature_min=log10temperature_min)
mcmc.run(context='paper', subtractions=[30, -1e-10])
diff --git a/examples/fully_coherent_search_using_MCMC_on_glitching_data.py b/examples/fully_coherent_search_using_MCMC_on_glitching_data.py
index 75c35cbd33573b335737771964d9b172fb7aefbc..3b9b60a3bbeb0f624027cebea6e9376ca483811e 100644
--- a/examples/fully_coherent_search_using_MCMC_on_glitching_data.py
+++ b/examples/fully_coherent_search_using_MCMC_on_glitching_data.py
@@ -26,7 +26,7 @@ nwalkers = 100
nsteps = [500, 500]
mcmc = MCMCSearch('fully_coherent_search_using_MCMC_on_glitching_data', 'data',
- sftfilepath='data/*_glitch*.sft',
+ sftfilepattern='data/*_glitch*.sft',
theta_prior=theta_prior, tref=tref, minStartTime=tstart, maxStartTime=tend,
nsteps=nsteps, nwalkers=nwalkers, ntemps=ntemps,
log10temperature_min=log10temperature_min)
diff --git a/examples/glitch_robust_search.py b/examples/glitch_robust_search.py
index 86e16b7736587f834b4549443c1824993bc0fbf5..731fb83a7fb3df59c1dcf98f4b528c62e1d2253e 100644
--- a/examples/glitch_robust_search.py
+++ b/examples/glitch_robust_search.py
@@ -17,7 +17,7 @@ Delta = np.radians(22.0144)
tref = tstart + .5 * Tspan
-sftfilepath = 'data/*glitching_signal*sft'
+sftfilepattern = 'data/*glitching_signal*sft'
F0_width = np.sqrt(3)/(np.pi*Tspan)
F1_width = np.sqrt(45/4.)/(np.pi*Tspan**2)
@@ -45,7 +45,7 @@ theta_prior = {'F0': {'type': 'unif',
}
search = pyfstat.MCMCGlitchSearch(
- label=label, outdir=outdir, sftfilepath=sftfilepath,
+ label=label, outdir=outdir, sftfilepattern=sftfilepattern,
theta_prior=theta_prior, nglitch=1, tref=tref, nsteps=[500, 500],
ntemps=3, log10temperature_min=-0.5, minStartTime=tstart,
maxStartTime=tstart+Tspan)
diff --git a/examples/semi_coherent_glitch_search_using_MCMC.py b/examples/semi_coherent_glitch_search_using_MCMC.py
index 789481de83b5fcd0670f44e1a39d09d39070af3d..f55c3429654c6e1ffe23f6ccfaa84d226718fa0e 100644
--- a/examples/semi_coherent_glitch_search_using_MCMC.py
+++ b/examples/semi_coherent_glitch_search_using_MCMC.py
@@ -31,7 +31,7 @@ nsteps = [5000, 1000, 1000]
mcmc = pyfstat.MCMCGlitchSearch(
'semi_coherent_glitch_search_using_MCMC', 'data',
- sftfilepath='data/*_glitch*sft', theta_prior=theta_prior, tref=tref,
+ sftfilepattern='data/*_glitch*sft', theta_prior=theta_prior, tref=tref,
tstart=tstart, tend=tend, nsteps=nsteps, nwalkers=nwalkers,
scatter_val=1e-10, nglitch=1, ntemps=ntemps,
log10temperature_min=log10temperature_min)
diff --git a/examples/semi_coherent_search_using_MCMC.py b/examples/semi_coherent_search_using_MCMC.py
index 86e4ecc2a87a9a4034032b212c8aa76539489965..4d08e3d64d4985e1dc5c56ebb9420eb4198d5cfe 100644
--- a/examples/semi_coherent_search_using_MCMC.py
+++ b/examples/semi_coherent_search_using_MCMC.py
@@ -25,7 +25,7 @@ nsteps = [500, 500, 500]
mcmc = pyfstat.MCMCSemiCoherentSearch(
label='semi_coherent_search_using_MCMC', outdir='data', nsegs=20,
- sftfilepath='data/*basic*sft', theta_prior=theta_prior, tref=tref,
+ sftfilepattern='data/*basic*sft', theta_prior=theta_prior, tref=tref,
minStartTime=tstart, maxStartTime=tend, nsteps=nsteps, nwalkers=nwalkers,
ntemps=ntemps, log10temperature_min=log10temperature_min)
mcmc.run()
diff --git a/examples/semi_coherent_twoglitch_search_using_MCMC.py b/examples/semi_coherent_twoglitch_search_using_MCMC.py
index 3e3a7d3bbe307b923372edb9952a4e1d3c0ba2b1..b467557320391cc5fc6bb8569823efa55314878d 100644
--- a/examples/semi_coherent_twoglitch_search_using_MCMC.py
+++ b/examples/semi_coherent_twoglitch_search_using_MCMC.py
@@ -34,7 +34,7 @@ nwalkers = 100
nsteps = [1000, 1000, 5000]
mcmc = pyfstat.MCMCGlitchSearch(
- 'semi_coherent_twoglitch_search', 'data', sftfilepath='data/*twoglitch*sft',
+ 'semi_coherent_twoglitch_search', 'data', sftfilepattern='data/*twoglitch*sft',
theta_prior=theta_prior, tref=tref, tstart=tstart,
tend=tend, nsteps=nsteps, nwalkers=nwalkers, scatter_val=1e-10, nglitch=2)
diff --git a/examples/sliding_window.py b/examples/sliding_window.py
index 34b4311ecce0152536edd68847b45bedf42ac55f..96ea6745b4ca5d8249b7ecedc4ad9955bfffbd12 100644
--- a/examples/sliding_window.py
+++ b/examples/sliding_window.py
@@ -27,7 +27,7 @@ data.make_data()
DeltaF0 = 1e-5
search = pyfstat.FrequencySlidingWindow(
- label='sliding_window', outdir='data', sftfilepath='data/*sliding_window*sft',
+ label='sliding_window', outdir='data', sftfilepattern='data/*sliding_window*sft',
F0s=[F0-DeltaF0, F0+DeltaF0, DeltaF0/100.], F1=F1, F2=0,
Alpha=Alpha, Delta=Delta, tref=tref, minStartTime=tstart,
maxStartTime=tend, window_size=25*86400, window_delta=1*86400)
diff --git a/examples/transient_search_using_MCMC.py b/examples/transient_search_using_MCMC.py
index 12125f0c237cbbd3f6bc6e58539a741f737aab22..62419c11086f5cd177250e02cc0c1f39a40a0e73 100644
--- a/examples/transient_search_using_MCMC.py
+++ b/examples/transient_search_using_MCMC.py
@@ -40,7 +40,7 @@ nsteps = [100, 100]
mcmc = pyfstat.MCMCTransientSearch(
label='transient_search', outdir='data',
- sftfilepath='data/*simulated_transient_signal*sft',
+ sftfilepattern='data/*simulated_transient_signal*sft',
theta_prior=theta_prior, tref=tref, minStartTime=minStartTime,
maxStartTime=maxStartTime, nsteps=nsteps, nwalkers=nwalkers, ntemps=ntemps,
log10temperature_min=log10temperature_min)
diff --git a/examples/weak_signal_follow_up.py b/examples/weak_signal_follow_up.py
index 5aa1e1d11f909c59a9e7c1de4d7eb44e86b98f1c..4c51c0d286f11f198bf7fd5b82114fc40b141425 100644
--- a/examples/weak_signal_follow_up.py
+++ b/examples/weak_signal_follow_up.py
@@ -55,7 +55,7 @@ nsteps = [100, 100]
mcmc = pyfstat.MCMCFollowUpSearch(
label='weak_signal_follow_up', outdir='data',
- sftfilepath='data/*'+data_label+'*sft', theta_prior=theta_prior, tref=tref,
+ sftfilepattern='data/*'+data_label+'*sft', theta_prior=theta_prior, tref=tref,
minStartTime=tstart, maxStartTime=tend, nwalkers=nwalkers, nsteps=nsteps,
ntemps=ntemps, log10temperature_min=log10temperature_min,
scatter_val=scatter_val)
diff --git a/pyfstat/core.py b/pyfstat/core.py
index 6a6fbdc7e0acb2b984739e9d2dfb00e534868a93..18eb009d0956fe49cb3ec17ee2a66129edd97ed5 100755
--- a/pyfstat/core.py
+++ b/pyfstat/core.py
@@ -174,16 +174,15 @@ class BaseSearchClass(object):
return thetas
def _get_list_of_matching_sfts(self):
- # first make sure we have a list of paths, to avoid
- # list comprehension trying to glob each single character
- sftfilepathlist = np.atleast_1d(self.sftfilepath)
- matches = [glob.glob(p) for p in sftfilepathlist]
+ """ Returns a list of sfts matching the sftfilepattern """
+ sftfilepatternlist = np.atleast_1d(self.sftfilepattern.split(';'))
+ matches = [glob.glob(p) for p in sftfilepatternlist]
matches = [item for sublist in matches for item in sublist]
if len(matches) > 0:
return matches
else:
raise IOError('No sfts found matching {}'.format(
- self.sftfilepath))
+ self.sftfilepattern))
class ComputeFstat(object):
@@ -193,7 +192,7 @@ class ComputeFstat(object):
sun_ephem_default = sun_ephem
@helper_functions.initializer
- def __init__(self, tref, sftfilepath=None, minStartTime=None,
+ def __init__(self, tref, sftfilepattern=None, minStartTime=None,
maxStartTime=None, binary=False, transient=True, BSGL=False,
detectors=None, minCoverFreq=None, maxCoverFreq=None,
earth_ephem=None, sun_ephem=None, injectSources=None,
@@ -203,8 +202,9 @@ class ComputeFstat(object):
----------
tref: int
GPS seconds of the reference time.
- sftfilepath: str
- File patern to match SFTs
+ sftfilepattern: str
+ Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+ mutiple patterns can be given separated by colons.
minStartTime, maxStartTime: float GPStime
Only use SFTs with timestemps starting from (including, excluding)
this epoch
@@ -250,7 +250,7 @@ class ComputeFstat(object):
def get_SFTCatalog(self):
if hasattr(self, 'SFTCatalog'):
return
- if self.sftfilepath is None:
+ if self.sftfilepattern is None:
for k in ['minStartTime', 'maxStartTime', 'detectors']:
if getattr(self, k) is None:
raise ValueError('You must provide "{}" to injectSources'
@@ -285,8 +285,8 @@ class ComputeFstat(object):
constraints.maxStartTime = lal.LIGOTimeGPS(self.maxStartTime)
logging.info('Loading data matching pattern {}'.format(
- self.sftfilepath))
- SFTCatalog = lalpulsar.SFTdataFind(self.sftfilepath, constraints)
+ self.sftfilepattern))
+ SFTCatalog = lalpulsar.SFTdataFind(self.sftfilepattern, constraints)
detector_names = list(set([d.header.name for d in SFTCatalog.data]))
self.detector_names = detector_names
SFT_timestamps = [d.header.epoch for d in SFTCatalog.data]
@@ -572,7 +572,7 @@ class ComputeFstat(object):
times = np.linspace(self.minStartTime, self.maxStartTime, N+1)[1:]
times = np.insert(times, 0, self.minStartTime + 86400/2.)
out = [predict_fstat(minStartTime=self.minStartTime, maxStartTime=t,
- sftfilepattern=self.sftfilepath, IFO=IFO,
+ sftfilepattern=self.sftfilepattern, IFO=IFO,
**pfs_input) for t in times]
pfs, pfs_sigma = np.array(out).T
return times, pfs, pfs_sigma
@@ -647,7 +647,7 @@ class SemiCoherentSearch(BaseSearchClass, ComputeFstat):
""" A semi-coherent search """
@helper_functions.initializer
- def __init__(self, label, outdir, tref, nsegs=None, sftfilepath=None,
+ def __init__(self, label, outdir, tref, nsegs=None, sftfilepattern=None,
binary=False, BSGL=False, minStartTime=None,
maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
detectors=None, earth_ephem=None, sun_ephem=None,
@@ -661,8 +661,9 @@ class SemiCoherentSearch(BaseSearchClass, ComputeFstat):
GPS seconds of the reference time, and start and end of the data.
nsegs: int
The (fixed) number of segments
- sftfilepath: str
- File patern to match SFTs
+ sftfilepattern: str
+ Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+ mutiple patterns can be given separated by colons.
For all other parameters, see pyfstat.ComputeFStat.
"""
@@ -776,7 +777,7 @@ class SemiCoherentGlitchSearch(BaseSearchClass, ComputeFstat):
@helper_functions.initializer
def __init__(self, label, outdir, tref, minStartTime, maxStartTime,
- nglitch=0, sftfilepath=None, theta0_idx=0, BSGL=False,
+ nglitch=0, sftfilepattern=None, theta0_idx=0, BSGL=False,
minCoverFreq=None, maxCoverFreq=None, assumeSqrtSX=None,
detectors=None, earth_ephem=None, sun_ephem=None,
SSBprec=None, injectSources=None):
@@ -790,8 +791,9 @@ class SemiCoherentGlitchSearch(BaseSearchClass, ComputeFstat):
nglitch: int
The (fixed) number of glitches; this can zero, but occasionally
this causes issue (in which case just use ComputeFstat).
- sftfilepath: str
- File patern to match SFTs
+ sftfilepattern: str
+ Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+ mutiple patterns can be given separated by colons.
theta0_idx, int
Index (zero-based) of which segment the theta refers to - uyseful
if providing a tight prior on theta to allow the signal to jump
diff --git a/pyfstat/grid_based_searches.py b/pyfstat/grid_based_searches.py
index 6eb8c2550834978d792bb6d1e6de0518a9d7ad42..8ef2ca13d04fc58bb5cbd67208df06d8f867862c 100644
--- a/pyfstat/grid_based_searches.py
+++ b/pyfstat/grid_based_searches.py
@@ -17,7 +17,7 @@ from core import tqdm, args, earth_ephem, sun_ephem, read_par
class GridSearch(BaseSearchClass):
""" Gridded search using ComputeFstat """
@helper_functions.initializer
- def __init__(self, label, outdir, sftfilepath, F0s=[0], F1s=[0], F2s=[0],
+ def __init__(self, label, outdir, sftfilepattern, F0s=[0], F1s=[0], F2s=[0],
Alphas=[0], Deltas=[0], tref=None, minStartTime=None,
maxStartTime=None, nsegs=1, BSGL=False, minCoverFreq=None,
maxCoverFreq=None, earth_ephem=None, sun_ephem=None,
@@ -28,8 +28,9 @@ class GridSearch(BaseSearchClass):
----------
label, outdir: str
A label and directory to read/write data from/to
- sftfilepath: str
- File patern to match SFTs
+ sftfilepattern: str
+ Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+ mutiple patterns can be given separated by colons.
F0s, F1s, F2s, delta_F0s, delta_F1s, tglitchs, Alphas, Deltas: tuple
Length 3 tuple describing the grid for each parameter, e.g
[F0min, F0max, dF0], for a fixed value simply give [F0]. Unless
@@ -56,7 +57,7 @@ class GridSearch(BaseSearchClass):
logging.info('Setting up search object')
if self.nsegs == 1:
self.search = ComputeFstat(
- tref=self.tref, sftfilepath=self.sftfilepath,
+ tref=self.tref, sftfilepattern=self.sftfilepattern,
minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
detectors=self.detectors, transient=False,
@@ -68,7 +69,7 @@ class GridSearch(BaseSearchClass):
else:
self.search = SemiCoherentSearch(
label=self.label, outdir=self.outdir, tref=self.tref,
- nsegs=self.nsegs, sftfilepath=self.sftfilepath,
+ nsegs=self.nsegs, sftfilepattern=self.sftfilepattern,
BSGL=self.BSGL, minStartTime=self.minStartTime,
maxStartTime=self.maxStartTime, minCoverFreq=self.minCoverFreq,
maxCoverFreq=self.maxCoverFreq, detectors=self.detectors,
@@ -106,7 +107,7 @@ class GridSearch(BaseSearchClass):
if os.path.isfile(self.out_file) is False:
logging.info('No old data found, continuing with grid search')
return False
- if self.sftfilepath is not None:
+ if self.sftfilepattern is not None:
oldest_sft = min([os.path.getmtime(f) for f in
self._get_list_of_matching_sfts()])
if os.path.getmtime(self.out_file) < oldest_sft:
@@ -275,7 +276,7 @@ class GridSearch(BaseSearchClass):
class GridUniformPriorSearch():
- def __init__(self, theta_prior, NF0, NF1, label, outdir, sftfilepath,
+ def __init__(self, theta_prior, NF0, NF1, label, outdir, sftfilepattern,
tref, minStartTime, maxStartTime, minCoverFreq=None,
maxCoverFreq=None, BSGL=False, detectors=None, nsegs=1):
dF0 = (theta_prior['F0']['upper'] - theta_prior['F0']['lower'])/NF0
@@ -283,7 +284,7 @@ class GridUniformPriorSearch():
F0s = [theta_prior['F0']['lower'], theta_prior['F0']['upper'], dF0]
F1s = [theta_prior['F1']['lower'], theta_prior['F1']['upper'], dF1]
self.search = GridSearch(
- label, outdir, sftfilepath, F0s=F0s, F1s=F1s, tref=tref,
+ label, outdir, sftfilepattern, F0s=F0s, F1s=F1s, tref=tref,
Alphas=[theta_prior['Alpha']], Deltas=[theta_prior['Delta']],
minStartTime=minStartTime, maxStartTime=maxStartTime, BSGL=BSGL,
detectors=detectors, minCoverFreq=minCoverFreq,
@@ -299,7 +300,7 @@ class GridUniformPriorSearch():
class GridGlitchSearch(GridSearch):
""" Grid search using the SemiCoherentGlitchSearch """
@helper_functions.initializer
- def __init__(self, label, outdir, sftfilepath=None, F0s=[0],
+ def __init__(self, label, outdir, sftfilepattern=None, F0s=[0],
F1s=[0], F2s=[0], delta_F0s=[0], delta_F1s=[0], tglitchs=None,
Alphas=[0], Deltas=[0], tref=None, minStartTime=None,
maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
@@ -310,8 +311,9 @@ class GridGlitchSearch(GridSearch):
----------
label, outdir: str
A label and directory to read/write data from/to
- sftfilepath: str
- File patern to match SFTs
+ sftfilepattern: str
+ Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+ mutiple patterns can be given separated by colons.
F0s, F1s, F2s, delta_F0s, delta_F1s, tglitchs, Alphas, Deltas: tuple
Length 3 tuple describing the grid for each parameter, e.g
[F0min, F0max, dF0], for a fixed value simply give [F0].
@@ -328,7 +330,7 @@ class GridGlitchSearch(GridSearch):
self.sun_ephem = self.sun_ephem_default
self.search = SemiCoherentGlitchSearch(
- label=label, outdir=outdir, sftfilepath=self.sftfilepath,
+ label=label, outdir=outdir, sftfilepattern=self.sftfilepattern,
tref=tref, minStartTime=minStartTime, maxStartTime=maxStartTime,
minCoverFreq=minCoverFreq, maxCoverFreq=maxCoverFreq,
earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
@@ -357,7 +359,7 @@ class GridGlitchSearch(GridSearch):
class FrequencySlidingWindow(GridSearch):
""" A sliding-window search over the Frequency """
@helper_functions.initializer
- def __init__(self, label, outdir, sftfilepath, F0s, F1, F2,
+ def __init__(self, label, outdir, sftfilepattern, F0s, F1, F2,
Alpha, Delta, tref, minStartTime=None,
maxStartTime=None, window_size=10*86400, window_delta=86400,
BSGL=False, minCoverFreq=None, maxCoverFreq=None,
@@ -368,8 +370,9 @@ class FrequencySlidingWindow(GridSearch):
----------
label, outdir: str
A label and directory to read/write data from/to
- sftfilepath: str
- File patern to match SFTs
+ sftfilepattern: str
+ Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+ mutiple patterns can be given separated by colons.
F0s: array
Frequency range
F1, F2, Alpha, Delta: float
@@ -397,7 +400,7 @@ class FrequencySlidingWindow(GridSearch):
def inititate_search_object(self):
logging.info('Setting up search object')
self.search = ComputeFstat(
- tref=self.tref, sftfilepath=self.sftfilepath,
+ tref=self.tref, sftfilepattern=self.sftfilepattern,
minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
detectors=self.detectors, transient=True,
@@ -473,7 +476,7 @@ class FrequencySlidingWindow(GridSearch):
class DMoff_NO_SPIN(GridSearch):
""" DMoff test using SSBPREC_NO_SPIN """
@helper_functions.initializer
- def __init__(self, par, label, outdir, sftfilepath, minStartTime=None,
+ def __init__(self, par, label, outdir, sftfilepattern, minStartTime=None,
maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
earth_ephem=None, sun_ephem=None, detectors=None,
injectSources=None, assumeSqrtSX=None):
@@ -485,8 +488,9 @@ class DMoff_NO_SPIN(GridSearch):
and 'tref') or a path to a .par file to read in the F0, F1 etc
label, outdir: str
A label and directory to read/write data from/to
- sftfilepath: str
- File patern to match SFTs
+ sftfilepattern: str
+ Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+ mutiple patterns can be given separated by colons.
minStartTime, maxStartTime: int
GPS seconds of the start time and end time
diff --git a/pyfstat/mcmc_based_searches.py b/pyfstat/mcmc_based_searches.py
index e41fe8c9a5a9e3ace293532eadf45090fcc051c8..64fa524ab33099538ed088bf351db6a9476fffe5 100644
--- a/pyfstat/mcmc_based_searches.py
+++ b/pyfstat/mcmc_based_searches.py
@@ -36,7 +36,7 @@ class MCMCSearch(core.BaseSearchClass):
@helper_functions.initializer
def __init__(self, label, outdir, theta_prior, tref, minStartTime,
- maxStartTime, sftfilepath=None, nsteps=[100, 100],
+ maxStartTime, sftfilepattern=None, nsteps=[100, 100],
nwalkers=100, ntemps=1, log10temperature_min=-5,
theta_initial=None, scatter_val=1e-10, rhohatmax=1000,
binary=False, BSGL=False, minCoverFreq=None, SSBprec=None,
@@ -46,7 +46,7 @@ class MCMCSearch(core.BaseSearchClass):
Parameters
label, outdir: str
A label and directory to read/write data from/to
- sftfilepath: str
+ sftfilepattern: str
Pattern to match SFTs using wildcards (*?) and ranges [0-9];
mutiple patterns can be given separated by colons.
theta_prior: dict
@@ -94,10 +94,10 @@ class MCMCSearch(core.BaseSearchClass):
os.mkdir(outdir)
self._add_log_file()
logging.info('Set-up MCMC search for model {}'.format(self.label))
- if sftfilepath:
- logging.info('Using data {}'.format(self.sftfilepath))
+ if sftfilepattern:
+ logging.info('Using data {}'.format(self.sftfilepattern))
else:
- logging.info('No sftfilepath given')
+ logging.info('No sftfilepattern given')
if injectSources:
logging.info('Inject sources: {}'.format(injectSources))
self.pickle_path = '{}/{}_saved_data.p'.format(self.outdir, self.label)
@@ -132,7 +132,7 @@ class MCMCSearch(core.BaseSearchClass):
def _initiate_search_object(self):
logging.info('Setting up search object')
self.search = core.ComputeFstat(
- tref=self.tref, sftfilepath=self.sftfilepath,
+ tref=self.tref, sftfilepattern=self.sftfilepattern,
minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
detectors=self.detectors, BSGL=self.BSGL, transient=False,
@@ -1112,7 +1112,7 @@ class MCMCSearch(core.BaseSearchClass):
logging.info('No pickled data found')
return False
- if self.sftfilepath is not None:
+ if self.sftfilepattern is not None:
oldest_sft = min([os.path.getmtime(f) for f in
self._get_list_of_matching_sfts()])
if os.path.getmtime(self.pickle_path) < oldest_sft:
@@ -1275,7 +1275,7 @@ class MCMCSearch(core.BaseSearchClass):
' --refTime={} --outputLoudest="{}/{}.loudest" '
'--minStartTime={} --maxStartTime={}').format(
params['Alpha'], params['Delta'], params['F0'],
- params['F1'], self.sftfilepath, params['tref'],
+ params['F1'], self.sftfilepattern, params['tref'],
self.outdir, self.label, self.minStartTime,
self.maxStartTime)
subprocess.call([cmd], shell=True)
@@ -1459,7 +1459,7 @@ class MCMCGlitchSearch(MCMCSearch):
)
@helper_functions.initializer
- def __init__(self, label, outdir, sftfilepath, theta_prior, tref,
+ def __init__(self, label, outdir, sftfilepattern, theta_prior, tref,
minStartTime, maxStartTime, nglitch=1, nsteps=[100, 100],
nwalkers=100, ntemps=1, log10temperature_min=-5,
theta_initial=None, scatter_val=1e-10, rhohatmax=1000,
@@ -1471,8 +1471,9 @@ class MCMCGlitchSearch(MCMCSearch):
----------
label, outdir: str
A label and directory to read/write data from/to
- sftfilepath: str
- File patern to match SFTs
+ sftfilepattern: str
+ Pattern to match SFTs using wildcards (*?) and ranges [0-9];
+ mutiple patterns can be given separated by colons.
theta_prior: dict
Dictionary of priors and fixed values for the search parameters.
For each parameters (key of the dict), if it is to be held fixed
@@ -1530,7 +1531,7 @@ class MCMCGlitchSearch(MCMCSearch):
self._add_log_file()
logging.info(('Set-up MCMC glitch search with {} glitches for model {}'
' on data {}').format(self.nglitch, self.label,
- self.sftfilepath))
+ self.sftfilepattern))
self.pickle_path = '{}/{}_saved_data.p'.format(self.outdir, self.label)
self._unpack_input_theta()
self.ndim = len(self.theta_keys)
@@ -1554,7 +1555,7 @@ class MCMCGlitchSearch(MCMCSearch):
def _initiate_search_object(self):
logging.info('Setting up search object')
self.search = core.SemiCoherentGlitchSearch(
- label=self.label, outdir=self.outdir, sftfilepath=self.sftfilepath,
+ label=self.label, outdir=self.outdir, sftfilepattern=self.sftfilepattern,
tref=self.tref, minStartTime=self.minStartTime,
maxStartTime=self.maxStartTime, minCoverFreq=self.minCoverFreq,
maxCoverFreq=self.maxCoverFreq, earth_ephem=self.earth_ephem,
@@ -1718,7 +1719,7 @@ class MCMCGlitchSearch(MCMCSearch):
class MCMCSemiCoherentSearch(MCMCSearch):
""" MCMC search for a signal using the semi-coherent ComputeFstat """
@helper_functions.initializer
- def __init__(self, label, outdir, theta_prior, tref, sftfilepath=None,
+ def __init__(self, label, outdir, theta_prior, tref, sftfilepattern=None,
nsegs=None, nsteps=[100, 100, 100], nwalkers=100,
binary=False, ntemps=1, log10temperature_min=-5,
theta_initial=None, scatter_val=1e-10, rhohatmax=1000,
@@ -1735,7 +1736,7 @@ class MCMCSemiCoherentSearch(MCMCSearch):
self._add_log_file()
logging.info(('Set-up MCMC semi-coherent search for model {} on data'
'{}').format(
- self.label, self.sftfilepath))
+ self.label, self.sftfilepattern))
self.pickle_path = '{}/{}_saved_data.p'.format(self.outdir, self.label)
self._unpack_input_theta()
self.ndim = len(self.theta_keys)
@@ -1767,7 +1768,7 @@ class MCMCSemiCoherentSearch(MCMCSearch):
logging.info('Setting up search object')
self.search = core.SemiCoherentSearch(
label=self.label, outdir=self.outdir, tref=self.tref,
- nsegs=self.nsegs, sftfilepath=self.sftfilepath, binary=self.binary,
+ nsegs=self.nsegs, sftfilepattern=self.sftfilepattern, binary=self.binary,
BSGL=self.BSGL, minStartTime=self.minStartTime,
maxStartTime=self.maxStartTime, minCoverFreq=self.minCoverFreq,
maxCoverFreq=self.maxCoverFreq, detectors=self.detectors,
@@ -2124,7 +2125,7 @@ class MCMCTransientSearch(MCMCSearch):
def _initiate_search_object(self):
logging.info('Setting up search object')
self.search = core.ComputeFstat(
- tref=self.tref, sftfilepath=self.sftfilepath,
+ tref=self.tref, sftfilepattern=self.sftfilepattern,
minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
earth_ephem=self.earth_ephem, sun_ephem=self.sun_ephem,
detectors=self.detectors, transient=True,
diff --git a/tests.py b/tests.py
index e11b5f5ddb7585dfee3db72b2192d567bafde5b4..22fe7a0ca8c8ad1ccdaa589b98c7fe0419a7d188 100644
--- a/tests.py
+++ b/tests.py
@@ -95,7 +95,7 @@ class TestComputeFstat(Test):
search = pyfstat.ComputeFstat(
tref=Writer.tref,
- sftfilepath='{}/*{}*sft'.format(Writer.outdir, Writer.label))
+ sftfilepattern='{}/*{}*sft'.format(Writer.outdir, Writer.label))
FS = search.run_computefstatistic_single_point(Writer.tstart,
Writer.tend,
Writer.F0,
@@ -113,7 +113,7 @@ class TestComputeFstat(Test):
search = pyfstat.ComputeFstat(
tref=Writer.tref, assumeSqrtSX=1,
- sftfilepath='{}/*{}*sft'.format(Writer.outdir, Writer.label))
+ sftfilepattern='{}/*{}*sft'.format(Writer.outdir, Writer.label))
FS = search.run_computefstatistic_single_point(Writer.tstart,
Writer.tend,
Writer.F0,
@@ -162,7 +162,7 @@ class TestSemiCoherentGlitchSearch(Test):
search = pyfstat.SemiCoherentGlitchSearch(
label=self.label, outdir=outdir,
- sftfilepath='{}/*{}*sft'.format(Writer.outdir, Writer.label),
+ sftfilepattern='{}/*{}*sft'.format(Writer.outdir, Writer.label),
tref=Writer.tref, minStartTime=Writer.tstart,
maxStartTime=Writer.tend, nglitch=1)
@@ -221,7 +221,7 @@ class TestMCMCSearch(Test):
search = pyfstat.MCMCSearch(
label=self.label, outdir=outdir, theta_prior=theta, tref=tref,
- sftfilepath='{}/*{}*sft'.format(Writer.outdir, Writer.label),
+ sftfilepattern='{}/*{}*sft'.format(Writer.outdir, Writer.label),
minStartTime=minStartTime, maxStartTime=maxStartTime,
nsteps=[100, 100], nwalkers=100, ntemps=2, log10temperature_min=-1)
search.setup_convergence_testing()